Todiramphus data filtering
Devon DeRaad
10/2/2021
#load packages
library(vcfR)
library(ggplot2)
library(adegenet)
library(SNPfiltR)
library(StAMPP)
#read in vcf as vcfR
#this has been pre-filtered using the command:
#vcftools --vcf populations.snps.vcf --out filt --max-missing .1 --recode --recode-INFO-all
#in order to make sure that the file can be read into Rstudio
vcfR <- read.vcfR("~/Desktop/todi.2022/populations.snps.vcf")
### check the metadata present in your vcf
vcfR
#read in sample info csv
sample.info<-read.csv("~/Desktop/todi.2022/todiramphus.subset.csv")
#make sure sampling file matches vcf
sample.info$id %in% colnames(vcfR@gt)[-1]
colnames(vcfR@gt)[-1] %in% sample.info$id
#if needed, subset sampling file to include only samples in vcf
#sample.info<-sample.info[sample.info$id %in% colnames(vcfR@gt)[-1],]
#reorder sampling file to match order of samples in vcf
sample.info<-sample.info[match(colnames(vcfR@gt)[-1], sample.info$id),]
sample.info$id == colnames(vcfR@gt)[-1]step 1: Implement quality filters that don’t involve missing data. This is because removing low data samples will alter percentage/quantile based missing data cutoffs, so we wait to implement those until after deciding on our final set of samples for downstream analysis
#hard filter to minimum depth of 5, and minimum genotype quality of 30
vcfR<-hard_filter(vcfR=vcfR, depth = 5, gq = 30)## 25.19% of genotypes fall below a read depth of 5 and were converted to NA## 1.6% of genotypes fall below a genotype quality of 30 and were converted to NAUse this function to filter for allele balance from Puritz SNP filtering tutorial “Allele balance: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous, we expect that the allele balance in our data (for real loci) should be close to 0.5”
#execute allele balance filter
vcfR<-filter_allele_balance(vcfR)## 9.4% of het genotypes (0.4% of all genotypes) fall outside of 0.25 - 0.75 allele balance ratio and were converted to NA
max depth filter (super high depth loci are likely multiple loci stuck together into a single paralogous locus).
#visualize and pick appropriate max depth cutoff
max_depth(vcfR)## cutoff is not specified, exploratory visualization will be generated.
## dashed line indicates a mean depth across all SNPs of 53.3
#filter vcf by the max depth cutoff you chose
vcfR<-max_depth(vcfR, maxdepth = 100)## maxdepth cutoff is specified, filtered vcfR object will be returned## 16.32% of SNPs were above a mean depth of 100 and were removed from the vcf
#check vcfR to see how many SNPs we have left
vcfR## ***** Object of Class vcfR *****
## 100 samples
## 347 CHROMs
## 186,091 variants
## Object size: 346.7 Mb
## 83.77 percent missing data
## ***** ***** *****Step 2: visualize missing data by sample. Check out the visualizations and make decision on which samples to keep for downstream analysis.
#run function to visualize samples
miss<-missing_by_sample(vcfR=vcfR)## No popmap provided
#histogram of number of SNPs called in each sample at a .5 SNP completeness cutoff
hist(miss$snps.retained[miss$filt == .5], breaks=50)
hist(miss$snps.retained[miss$filt == .5], breaks = 100)
#run function to drop samples above the threshold we want from the vcf
#(going with a very lenient cutoff here, can clean up bad samples down the line if needed)
vcfR<-missing_by_sample(vcfR=vcfR, cutoff = .95)## 13 samples are above a 0.95 missing data cutoff, and were removed from VCF
#remove invariant sites generated by sample trimming
vcfR<-min_mac(vcfR, min.mac = 1)## 55.03% of SNPs fell below a minor allele count of 1 and were removed from the VCF
### interrogate potential batch effects between runs
#interrogate batch effects between runs
#make a popmap where pop corresponds to the run the sample was on
batch.map<-sample.info[sample.info$id %in% colnames(vcfR@gt)[-1],c(1,2)]
colnames(batch.map)<-c("id","pop")
batch.map$pop<-as.factor(batch.map$pop)
#
assess_missing_data_pca(vcfR, popmap=batch.map, thresholds = .8, clustering = FALSE)## cutoff is specified, filtered vcfR object will be returned## 88.99% of SNPs fell below a completeness cutoff of 0.8 and were removed from the VCF
## [[1]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 -5.619609845 -9.82423507 -5.6631683 2.3753143742
## T_albicilla_22591 -5.717423623 -9.88407832 -5.7154664 2.2913904378
## T_albicilla_22592 -5.725967485 -9.80079329 -5.6737443 2.2766582539
## T_albicilla_22611 -4.177796800 -6.52279651 -3.9054526 1.5877132656
## T_albicilla_85104 -5.708193812 -9.87950482 -5.7359311 2.2453156553
## T_albicilla_85105 -5.661645281 -9.63322160 -5.5898141 2.2380803530
## T_chloris_12584 -2.884902571 -2.61955068 8.1764285 -5.4891731231
## T_chloris_12606 -2.896752624 -2.71588726 7.4748149 -5.6826017864
## T_chloris_13960 -2.716946308 -3.01561267 7.8290716 -8.3586270427
## T_chloris_14446 -2.736092002 -2.67819100 7.7600161 -7.9962968064
## T_chloris_20983 -2.752570486 -2.74826379 8.1036382 -8.0475199804
## T_chloris_22075 -3.006894426 -2.71251205 8.6099593 -5.6564391268
## T_chloris_23253 -2.907370296 -2.80075499 7.5707122 -4.9613340778
## T_chloris_23630 -2.856405177 -3.26997231 6.0917551 -7.8209230467
## T_chloris_23631 -1.461939224 -1.63024908 2.3286337 -3.1018058614
## T_chloris_23632 -2.854743492 -3.12448942 6.1080070 -7.5652742772
## T_chloris_24382 -2.741577175 -2.39812786 7.5527231 -5.2691158023
## T_chloris_24727 -2.730142432 -2.21793363 7.9485378 -4.8469893655
## T_chloris_67535_run1 -1.183571360 -0.65104200 2.1914300 -1.7665941618
## T_colonus_2003089 -3.236104984 -4.24886839 -0.1985283 -1.2274368611
## T_colonus_2003097 -3.252622113 -3.89149866 0.1863762 -1.7455248434
## T_colonus_2004070 -3.347047335 -4.33957576 -0.7487441 -2.0217012839
## T_leucopygius_32019 32.156637096 -7.68813066 -0.5236433 -0.0262991803
## T_leucopygius_32037 23.579958015 -5.75422262 -0.1235100 -0.2374579633
## T_leucopygius_34505 33.394251349 -7.82399769 -0.7054102 -0.0107270786
## T_leucopygius_34508 25.452165860 -6.40525065 -0.1552226 -0.3842523452
## T_leucopygius_DOT6654 31.315823162 -7.58135803 -0.5802596 0.0453003289
## T_sanctus_14877 0.144250151 7.01000299 -1.8642038 -0.2064376433
## T_sanctus_14879 -0.105022825 4.70947603 -1.3541403 -0.4080206729
## T_sanctus_24565 -0.058257699 7.30848609 -2.2670582 -0.0421039302
## T_sanctus_25117 0.275331255 6.68863347 -2.2125103 -0.1415831628
## T_sanctus_33267 0.269760832 7.37325536 -2.0721071 -0.0805246535
## T_sanctus_34636 0.257242492 7.86456970 -2.0315766 -0.6460816853
## T_sanctus_34659 -0.001213983 5.38260853 -1.5678394 0.3210876173
## T_sanctus_35549 0.143420240 6.49109106 -1.5351844 -0.1935377864
## T_sanctus_72545 0.166613468 6.95411287 -2.0090657 -0.0345705931
## T_sanctus_7567 0.209542062 7.69085141 -1.6149440 -0.1383699437
## T_sanctus_76296 -0.439995574 2.80075239 -0.5693844 -0.0009532665
## T_sanctus_B29435 0.021065569 6.52533731 -2.8007788 -0.5141668348
## T_sanctus_B32637 0.369714208 5.73534094 -1.5789716 -0.2771985148
## T_sanctus_B33280 0.414484926 7.25632583 -2.7907777 -0.4252982667
## T_sanctus_B34636 0.332471701 7.94210474 -2.1278755 -0.3392297193
## T_sanctus_B34659 0.660989994 7.99482034 -2.7835523 0.3155432926
## T_sanctus_B34946 0.195439801 7.27462921 -2.2758726 -0.3893582838
## T_sanctus_B43266 0.372644203 6.81233830 -2.2627966 0.1003798172
## T_sanctus_B50292 0.545072524 7.84750287 -2.3215220 0.1300588197
## T_sanctus_B50543 0.536775932 7.32920111 -2.5935509 -0.2584869904
## T_sanctus_B51072 0.273104652 7.37796029 -2.6418314 0.1314908067
## T_sanctus_B52989 0.164156664 3.91121780 -0.9070095 -0.3531468615
## T_sanctus_B53055 0.239746477 5.46171490 -1.6976754 0.1237263016
## T_sanctus_B53068 0.409551444 6.67313187 -1.7470300 -0.4709559068
## T_sanctus_B54673 0.145915084 7.31614939 -2.1007063 0.1242138379
## T_sanctus_B57402 0.406664600 6.50264593 -2.2997550 0.1292246397
## T_sanctus_B59372 0.276809468 7.33980547 -2.0514218 -0.0633623618
## T_sanctus_B60180 0.338370604 6.28172415 -2.0701641 -1.1810266008
## T_sanctus_B60181 0.515601356 7.80712980 -2.6216591 -0.3509515877
## T_sanctus_B60182 0.486913169 8.11988494 -2.2452738 0.0097850298
## T_sanctus_B60183 0.006026180 7.74815281 -2.5653264 -0.0683995764
## T_sanctus_B60184 0.372657771 8.48364907 -1.6589288 0.0758657577
## T_saurophagus_18929 -5.563403753 -9.63334822 -6.1244247 1.5574980378
## T_saurophagus_27804 -5.601051937 -9.62802681 -5.7903054 1.6476538340
## T_saurophagus_36179 -5.666060279 -9.95887314 -6.4454691 1.8148574239
## T_saurophagus_36283 -4.299852715 -7.87587918 -4.5328983 0.9515986165
## T_saurophagus_36284 -5.589355434 -9.76792204 -6.3393952 1.8041122463
## T_saurophagus_69666 -3.508363950 -5.66719078 -3.3335593 1.1405430604
## T_sordidus_B33717 -1.456349993 0.13617120 10.6417458 9.3865758073
## T_sordidus_B33718 -1.685771966 -0.03722172 10.5812971 8.9649628491
## T_sordidus_B33719 -1.395525575 0.05947083 9.4973363 8.8314406330
## T_sordidus_B33720 -1.149771876 0.25129289 9.2180778 8.5617732892
## T_sordidus_B44198 -1.529978048 -0.45861039 8.9517891 7.8208246186
## T_sordidus_B44295 -1.735515698 -0.56895009 8.8991997 8.0191337106
## T_sordidus_B44296 -1.476192151 -0.87763038 8.7500529 7.6275179921
## T_sordidus_B51462 -1.558207787 -0.19103853 9.7547024 8.9684620483
## T_tristrami_18953 -4.729052772 -7.66111196 -2.8790853 -0.3772306207
## T_tristrami_27723 -4.066837450 -6.99635502 -2.5383971 -0.2535373319
## T_tristrami_27752 -2.821682559 -5.22588119 -1.5838331 -0.5459367417
## T_tristrami_27792 -3.301542964 -5.21193993 -1.3370356 -0.5087129076
## T_tristrami_27793 -4.266958713 -6.73543498 -2.1798357 -0.2456332747
## T_tristrami_32049 -4.636546122 -7.36322135 -2.4202593 -0.6801370775
## T_tristrami_33253 -4.642341602 -7.36230901 -2.9006873 -0.1149905375
## T_tristrami_33839 0.462467250 7.35308849 -1.9572941 0.7809419349
## T_tristrami_33858 0.173492298 5.04864744 -1.2549830 0.0715561002
## T_tristrami_33864 0.249679458 7.38874575 -1.9840580 -0.7857049504
## T_tristrami_33867 0.535852411 7.42322819 -2.3030836 0.4258100168
## T_tristrami_33895 0.490705756 6.43634224 -1.8794549 -0.4896334902
## T_tristrami_36188 -4.135723647 -6.89745790 -2.6704629 -0.1070496166
## T_tristrami_6704 -4.764473559 -8.13307255 -3.2123944 0.0120145979
## PC5 pop missing
## T_albicilla_22581 -5.872573828 2 0.039509389
## T_albicilla_22591 -6.293191137 2 0.014219038
## T_albicilla_22592 -6.201250149 1 0.023119505
## T_albicilla_22611 -4.144467829 1 0.268425052
## T_albicilla_85104 -5.992700394 1 0.039400847
## T_albicilla_85105 -6.049712586 1 0.040377727
## T_chloris_12584 -1.135361618 1 0.008466298
## T_chloris_12606 -1.113174651 1 0.030283295
## T_chloris_13960 -2.181362549 1 0.024747639
## T_chloris_14446 -2.165722818 1 0.014978834
## T_chloris_20983 -2.316695124 1 0.016824053
## T_chloris_22075 -1.273559728 1 0.013567785
## T_chloris_23253 -1.115072761 1 0.059806795
## T_chloris_23630 -2.419407590 2 0.107891024
## T_chloris_23631 -0.974303777 1 0.543037013
## T_chloris_23632 -2.519934401 1 0.099641810
## T_chloris_24382 -1.449010952 1 0.072180614
## T_chloris_24727 -1.148200218 1 0.114620645
## T_chloris_67535_run1 -0.146057111 1 0.595897102
## T_colonus_2003089 4.292569904 1 0.109844785
## T_colonus_2003097 4.046463687 1 0.091066971
## T_colonus_2004070 4.700492860 1 0.110713123
## T_leucopygius_32019 -0.139754801 3 0.110278954
## T_leucopygius_32037 0.225811589 3 0.355367416
## T_leucopygius_34505 -0.356473578 3 0.094757408
## T_leucopygius_34508 0.153828882 3 0.297297297
## T_leucopygius_DOT6654 -0.306048834 3 0.146206447
## T_sanctus_14877 -0.460931802 1 0.036578747
## T_sanctus_14879 -0.231898620 1 0.320850971
## T_sanctus_24565 0.052571997 1 0.012807989
## T_sanctus_25117 0.011576109 1 0.073374579
## T_sanctus_33267 -0.302170056 1 0.022468251
## T_sanctus_34636 -0.637225767 1 0.019646152
## T_sanctus_34659 0.302937983 1 0.232280473
## T_sanctus_35549 0.139231811 1 0.073917291
## T_sanctus_72545 0.055748452 1 0.037664170
## T_sanctus_7567 0.043248927 1 0.022902420
## T_sanctus_76296 -0.099629939 1 0.477043308
## T_sanctus_B29435 -0.006436275 2 0.089764463
## T_sanctus_B32637 -0.102098696 2 0.268967763
## T_sanctus_B33280 -0.162668608 2 0.146206447
## T_sanctus_B34636 -0.579462141 2 0.029957669
## T_sanctus_B34659 0.255683907 2 0.040377727
## T_sanctus_B34946 -0.366631440 2 0.040377727
## T_sanctus_B43266 0.057328968 2 0.091392597
## T_sanctus_B50292 -0.253276174 2 0.079561489
## T_sanctus_B50543 0.118707875 2 0.018126560
## T_sanctus_B51072 0.171413815 2 0.013350700
## T_sanctus_B52989 -0.347880579 2 0.425811354
## T_sanctus_B53055 -0.444358656 2 0.243460328
## T_sanctus_B53068 -0.616644834 2 0.057418865
## T_sanctus_B54673 -0.558788075 2 0.037772712
## T_sanctus_B57402 -0.776929754 2 0.179963096
## T_sanctus_B59372 0.007531646 2 0.008574840
## T_sanctus_B60180 0.030839294 2 0.248453273
## T_sanctus_B60181 -0.042389851 2 0.080104201
## T_sanctus_B60182 0.155040704 2 0.010745685
## T_sanctus_B60183 -0.545305872 2 0.018235103
## T_sanctus_B60184 0.153601918 2 0.011722566
## T_saurophagus_18929 -2.878916587 1 0.018235103
## T_saurophagus_27804 -3.343678450 1 0.010420059
## T_saurophagus_36179 -3.286922258 2 0.013133616
## T_saurophagus_36283 -2.322460564 2 0.248019103
## T_saurophagus_36284 -3.213173648 2 0.006295452
## T_saurophagus_69666 -1.787985720 1 0.365244763
## T_sordidus_B33717 0.340856841 2 0.015630088
## T_sordidus_B33718 0.150296348 1 0.014653207
## T_sordidus_B33719 0.094791196 2 0.128839683
## T_sordidus_B33720 0.140565504 2 0.139910995
## T_sordidus_B44198 -0.020180007 2 0.124497992
## T_sordidus_B44295 0.259868209 1 0.058287203
## T_sordidus_B44296 0.081474251 2 0.155975252
## T_sordidus_B51462 -0.112640792 2 0.072723326
## T_tristrami_18953 7.978119685 1 0.023770759
## T_tristrami_27723 6.104783708 2 0.133507001
## T_tristrami_27752 4.858770144 2 0.378704005
## T_tristrami_27792 5.631588635 1 0.233474438
## T_tristrami_27793 7.055494182 1 0.052534462
## T_tristrami_32049 8.148850759 1 0.026701400
## T_tristrami_33253 8.646526214 1 0.007597959
## T_tristrami_33839 -0.379724289 2 0.018994899
## T_tristrami_33858 -0.396295021 2 0.275805926
## T_tristrami_33864 -0.170461442 2 0.015087377
## T_tristrami_33867 -0.129652402 2 0.017692391
## T_tristrami_33895 0.316046865 2 0.172690763
## T_tristrami_36188 7.399634991 2 0.123738196
## T_tristrami_6704 7.708556895 1 0.033431021#samples are clustering as species and within species by missing data, no indication of batch effects hereStep 3: Set the arbitrary missing data cutoff
We can visualize the effect that typical missing data cutoffs will have on both the number of SNPs retained and the total missing data in our entire dataset. We want to choose a cutoff that minimizes the overall missing data in the dataset, while maximizing the total number of loci retained.
#visualize missing data by SNP and the effect of various cutoffs on the missingness of each sample
missing_by_snp(vcfR)## cutoff is not specified, exploratory visualizations will be generated## Picking joint bandwidth of 0.0708
## filt missingness snps.retained
## 1 0.30 0.37867104 38368
## 2 0.50 0.26724679 25480
## 3 0.60 0.21218939 19571
## 4 0.65 0.18834898 17054
## 5 0.70 0.16464662 14578
## 6 0.75 0.13461192 11480
## 7 0.80 0.11262072 9213
## 8 0.85 0.08904051 6762
## 9 0.90 0.05966766 3747
## 10 0.95 0.03138883 1304
## 11 1.00 0.00000000 66#still need to target specific samples with too much missing data even at high filtering thresholds, for removal
#rerun missing by sample
miss<-missing_by_sample(vcfR=vcfR)## No popmap provided
#show me the samples with the most missing data at a 85% completeness threshold
filt<-miss[miss$filt == .8,]
filt[order(filt$snps.retained),]## indiv filt snps.retained
## 280 T_chloris_67535_run1 0.8 3723
## 276 T_chloris_23631 0.8 4210
## 299 T_sanctus_76296 0.8 4818
## 310 T_sanctus_B52989 0.8 5290
## 337 T_tristrami_27752 0.8 5724
## 326 T_saurophagus_69666 0.8 5848
## 285 T_leucopygius_32037 0.8 5939
## 290 T_sanctus_14879 0.8 6257
## 287 T_leucopygius_34508 0.8 6474
## 343 T_tristrami_33858 0.8 6672
## 301 T_sanctus_B32637 0.8 6735
## 265 T_albicilla_22611 0.8 6740
## 316 T_sanctus_B60180 0.8 6924
## 324 T_saurophagus_36283 0.8 6928
## 311 T_sanctus_B53055 0.8 6970
## 338 T_tristrami_27792 0.8 7062
## 295 T_sanctus_34659 0.8 7073
## 314 T_sanctus_B57402 0.8 7555
## 346 T_tristrami_33895 0.8 7622
## 333 T_sordidus_B44296 0.8 7776
## 288 T_leucopygius_DOT6654 0.8 7866
## 302 T_sanctus_B33280 0.8 7866
## 330 T_sordidus_B33720 0.8 7924
## 336 T_tristrami_27723 0.8 7983
## 329 T_sordidus_B33719 0.8 8026
## 331 T_sordidus_B44198 0.8 8066
## 347 T_tristrami_36188 0.8 8073
## 279 T_chloris_24727 0.8 8157
## 283 T_colonus_2004070 0.8 8193
## 284 T_leucopygius_32019 0.8 8197
## 281 T_colonus_2003089 0.8 8201
## 275 T_chloris_23630 0.8 8219
## 277 T_chloris_23632 0.8 8295
## 286 T_leucopygius_34505 0.8 8340
## 306 T_sanctus_B43266 0.8 8371
## 282 T_colonus_2003097 0.8 8374
## 300 T_sanctus_B29435 0.8 8386
## 317 T_sanctus_B60181 0.8 8475
## 307 T_sanctus_B50292 0.8 8480
## 296 T_sanctus_35549 0.8 8532
## 292 T_sanctus_25117 0.8 8537
## 334 T_sordidus_B51462 0.8 8543
## 278 T_chloris_24382 0.8 8548
## 274 T_chloris_23253 0.8 8662
## 332 T_sordidus_B44295 0.8 8676
## 312 T_sanctus_B53068 0.8 8684
## 339 T_tristrami_27793 0.8 8729
## 267 T_albicilla_85105 0.8 8841
## 304 T_sanctus_B34659 0.8 8841
## 305 T_sanctus_B34946 0.8 8841
## 262 T_albicilla_22581 0.8 8849
## 266 T_albicilla_85104 0.8 8850
## 313 T_sanctus_B54673 0.8 8865
## 297 T_sanctus_72545 0.8 8866
## 289 T_sanctus_14877 0.8 8876
## 348 T_tristrami_6704 0.8 8905
## 269 T_chloris_12606 0.8 8934
## 303 T_sanctus_B34636 0.8 8937
## 340 T_tristrami_32049 0.8 8967
## 270 T_chloris_13960 0.8 8985
## 335 T_tristrami_18953 0.8 8994
## 264 T_albicilla_22592 0.8 9000
## 298 T_sanctus_7567 0.8 9002
## 293 T_sanctus_33267 0.8 9006
## 294 T_sanctus_34636 0.8 9032
## 342 T_tristrami_33839 0.8 9038
## 319 T_sanctus_B60183 0.8 9045
## 321 T_saurophagus_18929 0.8 9045
## 308 T_sanctus_B50543 0.8 9046
## 345 T_tristrami_33867 0.8 9050
## 272 T_chloris_20983 0.8 9058
## 327 T_sordidus_B33717 0.8 9069
## 344 T_tristrami_33864 0.8 9074
## 271 T_chloris_14446 0.8 9075
## 328 T_sordidus_B33718 0.8 9078
## 263 T_albicilla_22591 0.8 9082
## 273 T_chloris_22075 0.8 9088
## 309 T_sanctus_B51072 0.8 9090
## 323 T_saurophagus_36179 0.8 9092
## 291 T_sanctus_24565 0.8 9095
## 320 T_sanctus_B60184 0.8 9105
## 318 T_sanctus_B60182 0.8 9114
## 322 T_saurophagus_27804 0.8 9117
## 315 T_sanctus_B59372 0.8 9134
## 268 T_chloris_12584 0.8 9135
## 341 T_tristrami_33253 0.8 9143
## 325 T_saurophagus_36284 0.8 9155#drop the three continuing outlier samples at a 85% SNP completeness threshold
vcfR<- vcfR[,colnames(vcfR@gt) != "T_chloris_67535_run1" &
colnames(vcfR@gt) != "T_chloris_23631" &
colnames(vcfR@gt) != "T_sanctus_76296" &
colnames(vcfR@gt) != "T_sanctus_B52989"]
#remove invariant SNPs
vcfR<-min_mac(vcfR, min.mac = 1)## 3.47% of SNPs fell below a minor allele count of 1 and were removed from the VCF
vcfR## ***** Object of Class vcfR *****
## 83 samples
## 194 CHROMs
## 80,776 variants
## Object size: 214.5 Mb
## 64.46 percent missing data
## ***** ***** *****#re-visualize missing data by SNP and the effect of various cutoffs on the missingness of each sample
missing_by_snp(vcfR)## cutoff is not specified, exploratory visualizations will be generated## Picking joint bandwidth of 0.0683
## filt missingness snps.retained
## 1 0.30 0.37361219 39441
## 2 0.50 0.25707739 26163
## 3 0.60 0.20532767 20689
## 4 0.65 0.18083119 18133
## 5 0.70 0.14973052 14917
## 6 0.75 0.12481566 12377
## 7 0.80 0.10038540 9910
## 8 0.85 0.07571551 7430
## 9 0.90 0.05149154 5011
## 10 0.95 0.02791287 2636
## 11 1.00 0.00000000 300#all samples look decent at high thresholds
#make popmap
popmap<-sample.info[sample.info$id %in% colnames(vcfR@gt)[-1],c(1,5)]
colnames(popmap)<-c("id","pop")
popmap$pop<-as.factor(popmap$pop)
#assess missing data effects on clustering
assess_missing_data_pca(vcfR = vcfR, popmap = popmap, thresholds = c(.75,.8,.85), clustering = FALSE)## cutoff is specified, filtered vcfR object will be returned## 84.68% of SNPs fell below a completeness cutoff of 0.75 and were removed from the VCF
## cutoff is specified, filtered vcfR object will be returned
## 87.73% of SNPs fell below a completeness cutoff of 0.8 and were removed from the VCF
## cutoff is specified, filtered vcfR object will be returned
## 90.8% of SNPs fell below a completeness cutoff of 0.85 and were removed from the VCF
## [[1]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 7.0121667 -11.0542908 -7.04969813 1.76177557
## T_albicilla_22591 7.3296157 -11.4351352 -7.32346820 1.85847022
## T_albicilla_22592 7.2348018 -11.1700446 -7.24323460 1.85246241
## T_albicilla_22611 5.1386906 -7.1723689 -4.81785836 1.40353643
## T_albicilla_85104 7.1254748 -10.8769395 -7.20980916 1.93330690
## T_albicilla_85105 7.0452229 -10.6757005 -6.98833498 1.92866178
## T_chloris_12584 4.1996443 -3.2481522 10.33987648 -6.38570656
## T_chloris_12606 3.9406958 -2.9281397 9.39164631 -6.66917818
## T_chloris_13960 3.8584281 -3.2334374 10.10877582 -9.42290305
## T_chloris_14446 3.9190017 -3.0409967 10.26880994 -9.12175722
## T_chloris_20983 3.9943601 -3.1548780 10.61499048 -9.12263727
## T_chloris_22075 4.1667635 -2.9617041 11.11217144 -6.65032619
## T_chloris_23253 3.7881375 -2.6992906 8.79958377 -5.56697016
## T_chloris_23630 3.5725535 -3.4315625 7.65171376 -7.74165518
## T_chloris_23632 3.9034378 -3.1958691 7.80865230 -7.72389003
## T_chloris_24382 3.6258084 -2.4778154 9.20699003 -6.30261635
## T_chloris_24727 3.6099238 -2.0625425 9.23297379 -5.41808640
## T_colonus_2003089 4.2576035 -4.2716136 0.05452408 -1.50333321
## T_colonus_2003097 4.1274821 -3.8523564 0.52533832 -1.76127104
## T_colonus_2004070 4.3872330 -4.4181938 -0.49481431 -2.10147416
## T_leucopygius_32019 -36.0984446 -10.9610646 -0.16264739 -0.34301185
## T_leucopygius_32037 -26.9886590 -8.0719500 0.21679712 -0.10753881
## T_leucopygius_34505 -37.6777214 -11.3757775 -0.22900681 -0.13009757
## T_leucopygius_34508 -28.8525385 -8.8433370 0.22757448 -0.47258652
## T_leucopygius_DOT6654 -35.2178405 -10.6458975 -0.24783081 -0.18743472
## T_sanctus_14877 -1.0189915 8.7750105 -2.31136481 -0.48397043
## T_sanctus_14879 -0.3966857 5.7087024 -1.37514512 -0.42178233
## T_sanctus_24565 -0.7403862 9.0319056 -2.73269358 -0.09900194
## T_sanctus_25117 -1.0037876 8.1538841 -2.32106467 -0.30825914
## T_sanctus_33267 -1.2352819 9.2364888 -2.39759861 -0.24571407
## T_sanctus_34636 -1.0026027 9.4172542 -2.51520808 -0.73129240
## T_sanctus_34659 -0.6532669 6.2523593 -1.51104271 0.26325900
## T_sanctus_35549 -0.7134587 7.6064671 -1.52748212 -0.44948412
## T_sanctus_72545 -0.7439014 8.4283878 -2.09711871 -0.30490331
## T_sanctus_7567 -0.9733815 9.1112542 -1.77959678 -0.34560827
## T_sanctus_B29435 -0.8748905 7.6783686 -2.71475844 -0.67520500
## T_sanctus_B32637 -0.9278681 6.1592727 -1.81590305 -0.32818595
## T_sanctus_B33280 -1.1366560 7.8913742 -2.70104518 -0.73747100
## T_sanctus_B34636 -1.0679826 9.2741254 -2.54336162 -0.43019430
## T_sanctus_B34659 -1.5171704 9.0087426 -3.28036161 0.02924152
## T_sanctus_B34946 -0.9303180 8.4874878 -2.30099439 -0.49666269
## T_sanctus_B43266 -0.9285970 7.5837405 -2.00258384 -0.16938556
## T_sanctus_B50292 -1.2446582 8.7264615 -2.58426202 0.01128691
## T_sanctus_B50543 -1.3810840 9.0736433 -3.09119936 -0.35788985
## T_sanctus_B51072 -1.1513129 8.9686316 -2.98727441 0.02972107
## T_sanctus_B53055 -0.6879519 5.7790918 -1.54661531 0.10431938
## T_sanctus_B53068 -1.0929738 7.9003911 -1.81822131 -0.53725489
## T_sanctus_B54673 -1.0327342 8.7533743 -2.37175274 -0.02151578
## T_sanctus_B57402 -1.0173929 6.9349038 -2.52868292 -0.09178685
## T_sanctus_B59372 -1.0430501 9.0809128 -2.50910701 -0.02139196
## T_sanctus_B60180 -0.9963268 6.8584212 -2.05663365 -1.28588228
## T_sanctus_B60181 -1.3582288 8.9361777 -2.54439385 -0.53112919
## T_sanctus_B60182 -1.2534007 9.6475167 -2.59761202 -0.19065148
## T_sanctus_B60183 -1.0176890 9.5823300 -2.93417989 -0.11884465
## T_sanctus_B60184 -1.3294372 10.1209940 -2.07810375 -0.05955343
## T_saurophagus_18929 7.2281086 -10.9098179 -7.46109373 1.00409292
## T_saurophagus_27804 7.2556589 -10.9250839 -7.10555919 1.15234095
## T_saurophagus_36179 7.2500499 -11.1966130 -7.78817532 1.28236450
## T_saurophagus_36283 4.9210242 -8.2600709 -5.08204344 0.38219205
## T_saurophagus_36284 7.3408384 -11.2655985 -7.75299084 1.24807181
## T_saurophagus_69666 4.5859862 -6.1436285 -3.95032627 0.95323619
## T_sordidus_B33717 2.4308976 -0.3574010 12.21204937 11.40416418
## T_sordidus_B33718 2.7135812 -0.5410739 11.76947083 11.04834654
## T_sordidus_B33719 2.0437040 -0.3728679 10.20051581 10.30936110
## T_sordidus_B33720 1.7606294 -0.2313845 9.57257426 10.10200976
## T_sordidus_B44198 2.1966048 -0.9117969 9.49920107 9.48311449
## T_sordidus_B44295 2.6154588 -1.0239365 9.57471312 9.64473976
## T_sordidus_B44296 2.0884795 -1.3383391 9.48026708 9.11609663
## T_sordidus_B51462 2.2855812 -0.5669639 10.19118574 10.87931271
## T_tristrami_18953 6.2914294 -8.4422248 -3.54263685 -0.32449540
## T_tristrami_27723 4.8349788 -7.1311052 -2.84121438 -0.44677527
## T_tristrami_27752 3.1781011 -5.1635096 -1.61197733 -0.60472586
## T_tristrami_27792 4.1754542 -5.4045458 -1.84282897 -0.52937686
## T_tristrami_27793 5.6018004 -7.2675229 -2.94909420 -0.17416183
## T_tristrami_32049 6.0872566 -8.1367206 -3.37177596 -0.56680938
## T_tristrami_33253 6.1795486 -8.2606669 -3.60049751 -0.14718975
## T_tristrami_33839 -1.2678297 8.8791525 -2.13036469 0.79961757
## T_tristrami_33858 -0.6110964 5.2662522 -1.42391134 -0.18530633
## T_tristrami_33864 -0.9786316 8.8575360 -2.59612022 -0.61507484
## T_tristrami_33867 -1.2432742 8.9285815 -2.79760735 0.60314561
## T_tristrami_33895 -1.1125745 7.0053857 -1.92210576 -0.36154634
## T_tristrami_36188 5.0516680 -7.3169378 -3.09902760 -0.32309989
## T_tristrami_6704 6.1661925 -8.6777152 -3.84898012 -0.13419089
## PC5 PC6 PC7 PC8
## T_albicilla_22581 -6.974209456 0.47557915 5.271767670 -4.871267198
## T_albicilla_22591 -7.439804837 0.33965724 5.275563711 -4.991129105
## T_albicilla_22592 -7.091362737 0.31384699 5.030229138 -4.790033906
## T_albicilla_22611 -4.507965860 0.34011826 3.836307094 -3.222900332
## T_albicilla_85104 -6.828484701 0.62837153 4.853771794 -3.993637062
## T_albicilla_85105 -6.880966999 0.54913464 4.877002823 -3.778448218
## T_chloris_12584 -1.615337405 -8.07473884 1.742439228 1.681234477
## T_chloris_12606 -1.559791878 -7.71762766 2.003367110 1.013225629
## T_chloris_13960 -2.140280850 8.24626850 -3.239752836 -2.434596008
## T_chloris_14446 -1.955476960 8.60966752 -3.490966758 -2.547877069
## T_chloris_20983 -2.249805511 8.21193975 -3.583149381 -2.746264759
## T_chloris_22075 -1.678574136 -7.85856998 1.427676722 1.424257741
## T_chloris_23253 -1.487966433 -7.07217561 1.712592440 1.358009482
## T_chloris_23630 -1.936352177 6.17126435 -2.927860012 -2.313578037
## T_chloris_23632 -2.193284591 6.09974144 -2.264857009 -2.034992481
## T_chloris_24382 -2.074950426 -8.26108158 2.131810539 1.661871518
## T_chloris_24727 -1.659291094 -8.07928652 1.809237216 1.366337465
## T_colonus_2003089 5.644245608 5.88093840 9.360861438 8.649461717
## T_colonus_2003097 5.382461580 5.85761416 9.059623626 8.699491313
## T_colonus_2004070 6.095712775 5.70210614 9.525439380 8.547828183
## T_leucopygius_32019 -0.122400996 -0.14787477 0.179067085 -0.027288792
## T_leucopygius_32037 0.218098969 0.36492252 -0.187055213 -0.492034495
## T_leucopygius_34505 -0.309476678 -0.21939178 0.278031292 0.303086909
## T_leucopygius_34508 0.294710206 -0.03820655 -0.311011248 -0.140900878
## T_leucopygius_DOT6654 -0.217097674 -0.14226868 0.114394503 0.288071568
## T_sanctus_14877 -0.504188466 -0.62042847 0.149599136 -0.120953266
## T_sanctus_14879 -0.261663345 -0.13068101 -0.376560186 0.314916148
## T_sanctus_24565 -0.046458884 0.07459296 -0.281177388 0.103281213
## T_sanctus_25117 -0.002890203 0.01178232 -0.390045502 0.401925453
## T_sanctus_33267 -0.449984703 -0.38712998 -0.001925164 -0.321173617
## T_sanctus_34636 -0.480214097 -0.06010353 0.670669123 -0.576807852
## T_sanctus_34659 0.065160647 0.35485713 -0.715376112 -0.082507059
## T_sanctus_35549 0.079846206 0.22428826 -0.463304646 -0.312843625
## T_sanctus_72545 0.198963983 0.31124328 -0.521408925 -0.502720948
## T_sanctus_7567 -0.313223738 -0.23040274 -0.162973137 -0.320062047
## T_sanctus_B29435 0.026845311 0.55153187 0.344218529 0.843419413
## T_sanctus_B32637 -0.448504196 -0.52886141 -0.009859801 0.019552303
## T_sanctus_B33280 -0.281910044 -0.16511347 -0.449527650 -0.611732864
## T_sanctus_B34636 -0.407504212 0.03613173 0.788453981 -0.405503728
## T_sanctus_B34659 -0.065463466 -0.01163201 -0.807757277 0.013726820
## T_sanctus_B34946 -0.351404874 -0.03018599 0.046067499 -0.379861082
## T_sanctus_B43266 0.048706787 -0.15337162 -0.497923736 0.444855022
## T_sanctus_B50292 -0.571741680 0.50055781 -0.636341333 -0.350799192
## T_sanctus_B50543 -0.053117871 -0.21142943 -0.458386035 0.042903893
## T_sanctus_B51072 0.041941388 0.05266011 0.587328964 -0.372740395
## T_sanctus_B53055 -0.492803373 -0.44759631 0.142000379 -0.135359458
## T_sanctus_B53068 -0.452906231 0.34557907 -1.030172279 -0.517170089
## T_sanctus_B54673 -0.599647058 0.28185079 -0.192729306 0.010769192
## T_sanctus_B57402 -0.861435022 0.06433312 -0.029523341 -0.456524451
## T_sanctus_B59372 0.338621678 -0.26223951 -1.445992904 -0.395736385
## T_sanctus_B60180 -0.175871262 -0.16534749 0.835797384 0.419357242
## T_sanctus_B60181 -0.404478268 -0.67001884 0.849140181 -0.384971942
## T_sanctus_B60182 -0.082777941 -0.37211787 0.288978300 0.132516336
## T_sanctus_B60183 -0.951129338 -0.56044299 0.712501069 -0.194828457
## T_sanctus_B60184 0.019217515 -0.36326401 -0.019615731 0.280199941
## T_saurophagus_18929 -3.458978224 -0.48579947 -6.713872965 6.720748592
## T_saurophagus_27804 -3.682462406 -0.48858985 -5.937245064 5.970456240
## T_saurophagus_36179 -3.777696352 -0.53209163 -6.814187280 6.757433169
## T_saurophagus_36283 -2.309036752 -0.41652129 -4.643458226 4.118826703
## T_saurophagus_36284 -3.898775567 -0.57689696 -6.639273584 6.613264973
## T_saurophagus_69666 -2.011394923 -0.17370221 -3.862742977 3.725787977
## T_sordidus_B33717 0.019705336 0.78409681 -0.610854570 0.176995063
## T_sordidus_B33718 -0.202323938 1.09856953 -0.990441284 0.111789521
## T_sordidus_B33719 0.022487243 0.55930818 -0.817762566 0.154216026
## T_sordidus_B33720 -0.216260445 -0.13739699 -0.590534924 0.214911034
## T_sordidus_B44198 0.065996838 1.21834939 0.158539810 -0.369897638
## T_sordidus_B44295 0.176167071 0.93200915 0.186181967 -0.395637432
## T_sordidus_B44296 -0.173238884 1.07649976 -0.148579866 -0.351299188
## T_sordidus_B51462 -0.391114399 0.32077596 -0.529004889 -0.160475490
## T_tristrami_18953 9.226168771 -1.53288090 -1.826591899 -3.232734336
## T_tristrami_27723 6.647924648 -1.29326237 -1.139394022 -2.649409239
## T_tristrami_27752 4.872910759 -1.04908717 -0.688799762 -1.363225975
## T_tristrami_27792 5.992636466 -0.44711550 0.352831469 -2.046957139
## T_tristrami_27793 7.790159661 -1.63664456 -0.875010298 -3.318660763
## T_tristrami_32049 9.649967824 -1.23907559 -1.552762539 -3.606579525
## T_tristrami_33253 10.327562319 -1.55535025 -1.952473389 -3.443176301
## T_tristrami_33839 -0.500343812 0.10630646 -1.066312892 -0.503730306
## T_tristrami_33858 -0.524608591 0.14730857 0.012545070 -0.009221095
## T_tristrami_33864 -0.212115185 -0.72595869 -0.160067984 -0.652726757
## T_tristrami_33867 -0.027162111 0.38570494 -0.185308282 0.503151098
## T_tristrami_33895 0.238406919 0.64124395 0.589103524 0.543462318
## T_tristrami_36188 8.031363953 -1.41995987 -1.399678685 -3.140151718
## T_tristrami_6704 9.051720799 -1.17882974 -1.563528337 -3.560213996
## PC9 PC10 pop missing
## T_albicilla_22581 -0.2003713363 0.29997485 albicilla 0.05865719
## T_albicilla_22591 -0.1640565007 0.28140272 albicilla 0.01769411
## T_albicilla_22592 -0.2807100996 0.27766683 albicilla 0.03805446
## T_albicilla_22611 0.2106154151 0.26241912 albicilla 0.29878000
## T_albicilla_85104 -0.2067801883 0.19515839 albicilla 0.05849560
## T_albicilla_85105 -0.1103777375 0.15845476 albicilla 0.06011150
## T_chloris_12584 0.2780921007 0.19694020 chloris 0.01413913
## T_chloris_12606 0.0451716103 0.28969596 chloris 0.04371011
## T_chloris_13960 -0.3546547301 -0.89845140 chloris 0.04257898
## T_chloris_14446 -0.4545858200 -0.39590621 chloris 0.02205704
## T_chloris_20983 -0.3069659936 -0.57081054 chloris 0.02238022
## T_chloris_22075 -0.0455745598 0.48731295 chloris 0.01591662
## T_chloris_23253 0.1216404714 0.59307337 chloris 0.11012362
## T_chloris_23630 0.2024514286 -0.07964462 chloris 0.17451725
## T_chloris_23632 0.3682890249 0.27665226 chloris 0.13565484
## T_chloris_24382 -0.0006162337 0.49643673 chloris 0.10527592
## T_chloris_24727 0.3190902678 0.33982414 chloris 0.15035954
## T_colonus_2003089 -0.2508650684 0.46740898 colonus 0.13840187
## T_colonus_2003097 0.1517822161 0.57708436 colonus 0.13775551
## T_colonus_2004070 0.0799190312 0.32125531 colonus 0.14009857
## T_leucopygius_32019 0.0395610553 0.07604338 leucopygius 0.13226145
## T_leucopygius_32037 -0.0399074733 -0.29057141 leucopygius 0.36818292
## T_leucopygius_34505 -0.0804982134 0.26214961 leucopygius 0.11222429
## T_leucopygius_34508 -0.3892514531 -0.85743491 leucopygius 0.31671649
## T_leucopygius_DOT6654 0.5944954740 0.20798953 leucopygius 0.17168942
## T_sanctus_14877 -4.8834503659 -6.23255390 sanctus 0.05582936
## T_sanctus_14879 -1.8693697155 -1.91893545 sanctus 0.34442918
## T_sanctus_24565 1.0616152540 1.40023305 sanctus 0.02197625
## T_sanctus_25117 1.1358630712 0.81916206 sanctus 0.09267189
## T_sanctus_33267 0.2785348386 1.53282452 sanctus 0.03175244
## T_sanctus_34636 14.2671174865 -6.00670556 sanctus 0.03506504
## T_sanctus_34659 -0.9113232729 4.58440724 sanctus 0.26638119
## T_sanctus_35549 0.8871769683 1.16737732 sanctus 0.11133554
## T_sanctus_72545 -0.5512637421 1.31217989 sanctus 0.05534459
## T_sanctus_7567 -0.9343093908 3.10327462 sanctus 0.03902400
## T_sanctus_B29435 -0.2363037405 0.91096815 sanctus 0.14696615
## T_sanctus_B32637 -0.7253746413 1.75669068 sanctus 0.34539872
## T_sanctus_B33280 -0.4354222409 3.48235453 sanctus 0.22178234
## T_sanctus_B34636 14.0743092953 -5.65615374 sanctus 0.05833401
## T_sanctus_B34659 -0.9399070112 6.73862493 sanctus 0.07360427
## T_sanctus_B34946 1.2649495237 1.02179730 sanctus 0.07045326
## T_sanctus_B43266 -0.8204736989 1.49868467 sanctus 0.14664297
## T_sanctus_B50292 -0.5616866900 4.27131006 sanctus 0.12902965
## T_sanctus_B50543 0.0344275234 2.12697711 sanctus 0.02092591
## T_sanctus_B51072 -0.7494517090 1.63222564 sanctus 0.02221863
## T_sanctus_B53055 0.6574821479 0.84106042 sanctus 0.31607013
## T_sanctus_B53068 0.7893978559 2.43561026 sanctus 0.08855135
## T_sanctus_B54673 -0.0739832809 2.04908235 sanctus 0.07408904
## T_sanctus_B57402 -0.2483205042 1.57331901 sanctus 0.25143411
## T_sanctus_B59372 0.1568147308 2.01866721 sanctus 0.01413913
## T_sanctus_B60180 -2.7281457659 -4.23101791 sanctus 0.32705825
## T_sanctus_B60181 -4.5021158621 -6.05988781 sanctus 0.13169589
## T_sanctus_B60182 -3.4365229504 -7.20617141 sanctus 0.01583582
## T_sanctus_B60183 -5.4242838983 -8.34937473 sanctus 0.02763190
## T_sanctus_B60184 -5.3788043730 -6.92986257 sanctus 0.01672457
## T_saurophagus_18929 0.2034109133 -0.35435197 saurophagus 0.03716571
## T_saurophagus_27804 0.3172567005 -0.52659399 saurophagus 0.02431930
## T_saurophagus_36179 0.2658898175 -0.50946618 saurophagus 0.02682395
## T_saurophagus_36283 0.0815378888 -0.40752972 saurophagus 0.32180658
## T_saurophagus_36284 0.2323698839 -0.52562086 saurophagus 0.01123051
## T_saurophagus_69666 0.0977589240 -0.25785324 saurophagus 0.37852468
## T_sordidus_B33717 -0.0542296397 -0.43418304 sordidus 0.02730872
## T_sordidus_B33718 0.1721330922 0.14322501 sordidus 0.02286499
## T_sordidus_B33719 0.6542731642 -0.52912886 sordidus 0.19229215
## T_sordidus_B33720 0.4548270865 -0.64597532 sordidus 0.20255312
## T_sordidus_B44198 0.1101022682 0.14736387 sordidus 0.18712127
## T_sordidus_B44295 -0.5240656865 0.22372566 sordidus 0.09412620
## T_sordidus_B44296 -0.2630655306 -0.11568020 sordidus 0.22008564
## T_sordidus_B51462 -0.1771055517 -0.13174051 sordidus 0.11691040
## T_tristrami_18953 0.0467837275 -0.23211872 tristrami 0.04080149
## T_tristrami_27723 0.1189185718 -0.17116028 tristrami 0.19544316
## T_tristrami_27752 0.2674676879 -0.08680509 tristrami 0.45810778
## T_tristrami_27792 -0.3654840987 -0.50074421 tristrami 0.29708330
## T_tristrami_27793 -0.3091475000 -0.15545798 tristrami 0.09008645
## T_tristrami_32049 0.5083792115 0.22514162 tristrami 0.03967036
## T_tristrami_33253 -0.0808743448 -0.16771567 tristrami 0.01203846
## T_tristrami_33839 1.0237599502 1.78936200 tristrami 0.03417629
## T_tristrami_33858 -0.8905985696 0.93067931 tristrami 0.35283187
## T_tristrami_33864 -0.6428311767 2.68466676 tristrami 0.02092591
## T_tristrami_33867 -0.2194380943 2.51237180 tristrami 0.02965177
## T_tristrami_33895 0.3739009477 1.32236686 tristrami 0.24715198
## T_tristrami_36188 0.2228433099 -0.45530682 tristrami 0.17847621
## T_tristrami_6704 -0.3478414825 -0.43176253 tristrami 0.06188899
##
## [[2]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 6.092947696 -10.072082827 -5.955672604 2.38848790
## T_albicilla_22591 6.220846982 -10.164918610 -5.995341116 2.30394461
## T_albicilla_22592 6.205398580 -10.066810857 -5.907150214 2.28911882
## T_albicilla_22611 4.440754567 -6.492130635 -3.963400516 1.54476154
## T_albicilla_85104 6.172358440 -10.066497872 -5.915553310 2.30328175
## T_albicilla_85105 6.109579562 -9.795865850 -5.831407772 2.33362104
## T_chloris_12584 3.230539703 -2.695106240 8.625426954 -5.94335385
## T_chloris_12606 3.142689903 -2.545845234 7.859712981 -6.27507146
## T_chloris_13960 3.035768301 -3.031292928 8.194600204 -8.92521330
## T_chloris_14446 3.061330574 -2.685705526 8.296823078 -8.59335736
## T_chloris_20983 3.098933715 -2.718770393 8.725212630 -8.66144046
## T_chloris_22075 3.291518911 -2.621846442 9.103738068 -6.17076720
## T_chloris_23253 3.082581783 -2.546130203 7.700124510 -5.38955177
## T_chloris_23630 3.101882443 -3.232118976 6.317223794 -7.95647414
## T_chloris_23632 3.069000344 -3.031121716 6.314523671 -7.79416245
## T_chloris_24382 2.901761931 -2.204895201 7.782230794 -5.83967492
## T_chloris_24727 2.921185491 -2.033089433 8.001002891 -5.27277329
## T_colonus_2003089 3.456613287 -4.144649375 -0.233417105 -1.37180859
## T_colonus_2003097 3.462898459 -3.804279239 0.185419338 -1.76115422
## T_colonus_2004070 3.597268806 -4.419759990 -0.741049927 -2.04163632
## T_leucopygius_32019 -32.967578551 -8.677047697 -0.423972137 -0.08124960
## T_leucopygius_32037 -23.892628848 -6.359954685 0.006619215 -0.22829750
## T_leucopygius_34505 -34.275036734 -8.877413289 -0.574109545 -0.02606897
## T_leucopygius_34508 -26.050806383 -7.220040359 -0.102190186 -0.43485895
## T_leucopygius_DOT6654 -32.050581053 -8.492931925 -0.478400373 -0.05869077
## T_sanctus_14877 -0.369307461 7.433510144 -1.981294403 -0.21007325
## T_sanctus_14879 -0.001792175 4.863881249 -1.294683592 -0.37802636
## T_sanctus_24565 -0.119730890 7.760456735 -2.472513231 -0.05545290
## T_sanctus_25117 -0.525087704 7.210789913 -2.232622386 -0.13326772
## T_sanctus_33267 -0.560090453 7.926831761 -2.185049308 -0.09418472
## T_sanctus_34636 -0.455528476 8.300712876 -2.035397363 -0.79828856
## T_sanctus_34659 -0.085473957 5.539518329 -1.496671401 0.27774286
## T_sanctus_35549 -0.349372104 6.830507783 -1.474377748 -0.26433323
## T_sanctus_72545 -0.334070083 7.225620782 -1.928113392 -0.13126942
## T_sanctus_7567 -0.413790790 8.017743239 -1.635983210 -0.23995738
## T_sanctus_B29435 -0.272230971 6.870347595 -2.792770429 -0.42362772
## T_sanctus_B32637 -0.582569627 6.063104091 -1.788794347 -0.27244556
## T_sanctus_B33280 -0.720847551 7.707582185 -2.903556447 -0.29837177
## T_sanctus_B34636 -0.518050241 8.314336391 -2.171000719 -0.44066968
## T_sanctus_B34659 -0.873178875 8.365504803 -2.985199271 0.33168370
## T_sanctus_B34946 -0.371387960 7.433289384 -2.388533633 -0.18485581
## T_sanctus_B43266 -0.587459750 7.127769015 -2.249127304 0.01933968
## T_sanctus_B50292 -0.735782256 8.104274163 -2.323412713 0.32488903
## T_sanctus_B50543 -0.745892033 7.784955042 -2.682691025 -0.37450259
## T_sanctus_B51072 -0.486771124 7.792610873 -2.711690390 0.12628164
## T_sanctus_B53055 -0.365481495 5.609552765 -1.737803804 0.13685896
## T_sanctus_B53068 -0.599289708 7.020652304 -1.882806275 -0.47386086
## T_sanctus_B54673 -0.425965671 7.820207754 -2.223981319 0.03582019
## T_sanctus_B57402 -0.581305750 6.711352582 -2.373977292 0.16956998
## T_sanctus_B59372 -0.508711070 7.745063631 -2.018251380 -0.16938789
## T_sanctus_B60180 -0.592156473 6.571230042 -2.096035658 -1.22488965
## T_sanctus_B60181 -0.749659967 8.191265116 -2.576617125 -0.29578770
## T_sanctus_B60182 -0.699830922 8.483392786 -2.379503234 0.02888877
## T_sanctus_B60183 -0.267590419 8.228949949 -2.661716968 -0.06147706
## T_sanctus_B60184 -0.616697779 8.842604362 -1.719872193 -0.03534484
## T_saurophagus_18929 6.046950695 -9.860352523 -6.337639804 1.39873909
## T_saurophagus_27804 6.084444783 -9.917360528 -6.023092278 1.53425991
## T_saurophagus_36179 6.153311020 -10.166078589 -6.655676298 1.64627183
## T_saurophagus_36283 4.653765564 -8.066550258 -4.764132979 0.87080513
## T_saurophagus_36284 6.108329355 -10.044485206 -6.578631808 1.64862526
## T_saurophagus_69666 3.778596643 -5.689075096 -3.389871922 1.07990258
## T_sordidus_B33717 1.710584209 0.007376488 11.301956529 9.62029290
## T_sordidus_B33718 1.960771478 -0.186633023 11.195432854 9.26310280
## T_sordidus_B33719 1.591110360 -0.075682701 10.146295302 8.89320812
## T_sordidus_B33720 1.359780933 0.115049937 9.758664811 8.72742632
## T_sordidus_B44198 1.764694112 -0.567649821 9.553593498 7.97497298
## T_sordidus_B44295 1.961721835 -0.666418941 9.354633313 8.16554984
## T_sordidus_B44296 1.697766866 -0.954688141 9.306748401 7.76920150
## T_sordidus_B51462 1.825043052 -0.311243345 10.341448464 9.26415049
## T_tristrami_18953 5.165352673 -7.886499732 -2.999345747 -0.36478029
## T_tristrami_27723 4.410387948 -7.099961957 -2.635239677 -0.35657664
## T_tristrami_27752 3.046458866 -5.304486556 -1.646404905 -0.59487589
## T_tristrami_27792 3.482730954 -5.210578704 -1.528196339 -0.55670766
## T_tristrami_27793 4.614354064 -6.925410336 -2.368579825 -0.29720527
## T_tristrami_32049 5.037225767 -7.584817214 -2.526045769 -0.67842502
## T_tristrami_33253 5.032052514 -7.639138251 -3.021346776 -0.26461246
## T_tristrami_33839 -0.743700965 7.854736856 -1.970162095 0.80487127
## T_tristrami_33858 -0.333295744 5.245240109 -1.436376007 0.06680060
## T_tristrami_33864 -0.539337525 7.875852136 -2.317173630 -0.73369557
## T_tristrami_33867 -0.773127314 7.907570238 -2.453380649 0.46959678
## T_tristrami_33895 -0.678606957 6.722501307 -1.790068637 -0.34217194
## T_tristrami_36188 4.467389684 -7.120125556 -2.806638175 -0.14495414
## T_tristrami_6704 5.171120959 -8.348402734 -3.297715612 -0.09238323
## PC5 PC6 PC7 PC8
## T_albicilla_22581 -6.298258306 0.62767667 5.766140254 3.1522279346
## T_albicilla_22591 -6.661436001 0.52057293 5.720592539 3.0148091100
## T_albicilla_22592 -6.530661360 0.51032944 5.387559140 2.7968230699
## T_albicilla_22611 -4.161097444 0.49808556 3.848194835 1.7914694594
## T_albicilla_85104 -6.418281615 0.73243799 5.212044240 2.2921457041
## T_albicilla_85105 -6.367335627 0.63730359 5.177882620 2.1030001686
## T_chloris_12584 -1.346260145 -7.44350309 1.429590297 -1.8471395455
## T_chloris_12606 -1.372209202 -7.01624354 2.016043671 -1.3414731624
## T_chloris_13960 -2.291606717 7.11573717 -2.545291915 2.9115131827
## T_chloris_14446 -2.238240611 7.48317644 -2.439468281 2.8539150708
## T_chloris_20983 -2.413355742 6.91642292 -2.567757845 3.0885926620
## T_chloris_22075 -1.395107149 -6.92663668 1.184460449 -1.4387477513
## T_chloris_23253 -1.280449810 -6.36062656 1.377723238 -1.5211220400
## T_chloris_23630 -2.105815436 5.64335992 -2.444800087 2.5127372704
## T_chloris_23632 -2.335990895 5.38756884 -1.988529781 2.2928868305
## T_chloris_24382 -1.672960267 -7.46823986 1.647887946 -1.9049276810
## T_chloris_24727 -1.369090078 -7.32494118 1.760088241 -1.8398583967
## T_colonus_2003089 4.556137144 5.65844907 5.446864540 -9.8905595009
## T_colonus_2003097 4.376180023 5.67363585 5.208693125 -9.8786542790
## T_colonus_2004070 4.940357997 5.44277126 5.523089740 -9.8266482126
## T_leucopygius_32019 -0.208979823 -0.19608752 0.152323299 0.0237044028
## T_leucopygius_32037 0.191822272 0.31759262 -0.022057316 0.4342300366
## T_leucopygius_34505 -0.340673326 -0.23389526 0.156378911 -0.2538666268
## T_leucopygius_34508 0.130415173 -0.01620895 -0.121464077 0.0971132603
## T_leucopygius_DOT6654 -0.340733171 -0.09156867 -0.024493439 -0.1456255208
## T_sanctus_14877 -0.396073291 -0.45865761 0.494609458 0.0046867983
## T_sanctus_14879 -0.384883093 -0.02661100 -0.078237746 -0.2640684134
## T_sanctus_24565 0.079146832 -0.44774355 -0.451492043 0.1746052842
## T_sanctus_25117 0.044740188 -0.11856254 -0.517228503 -0.3446927897
## T_sanctus_33267 -0.341914436 -0.39864399 0.283247174 0.1389867818
## T_sanctus_34636 -0.668575504 -0.33533261 -0.024207452 0.5754392783
## T_sanctus_34659 0.223679726 0.30296760 -0.582525565 0.1556119538
## T_sanctus_35549 0.174653357 0.26327997 -0.189689627 0.0839633301
## T_sanctus_72545 0.088661056 0.24662732 -0.095743233 0.3489033770
## T_sanctus_7567 -0.094328440 -0.29175827 0.183806498 0.0887991455
## T_sanctus_B29435 0.072382414 0.46654923 -0.008587424 -0.5024098800
## T_sanctus_B32637 -0.219119065 -0.46086263 -0.003509084 0.0319698111
## T_sanctus_B33280 -0.157095801 -0.21437787 -0.332960078 0.6449317490
## T_sanctus_B34636 -0.586933315 -0.20701998 -0.000329519 0.5172166964
## T_sanctus_B34659 0.131030234 -0.20565258 -0.723215127 0.1459195176
## T_sanctus_B34946 -0.430753989 -0.25362266 -0.102314511 0.5957843893
## T_sanctus_B43266 0.151248600 -0.31561906 -0.108762223 -0.2422098124
## T_sanctus_B50292 -0.279941189 0.26987841 -0.447423484 0.5901838003
## T_sanctus_B50543 0.131909887 0.01359181 -0.325014885 -0.0888047842
## T_sanctus_B51072 0.149518824 0.22766399 0.714767168 0.1242419951
## T_sanctus_B53055 -0.438741474 -0.45650230 -0.026417158 0.3900021051
## T_sanctus_B53068 -0.482478460 0.22148353 -0.646424462 0.4023573925
## T_sanctus_B54673 -0.666217247 0.27873101 -0.281325787 -0.0552076031
## T_sanctus_B57402 -0.751204434 0.01373909 -0.236577881 0.5704562142
## T_sanctus_B59372 0.081713228 -0.31080489 -0.932551951 0.5477837722
## T_sanctus_B60180 -0.047354638 0.07012784 0.793931136 -0.4222468465
## T_sanctus_B60181 -0.209883057 -0.31835588 1.203855505 0.3992346960
## T_sanctus_B60182 0.091657079 -0.05905250 0.450250745 0.0009571224
## T_sanctus_B60183 -0.722978879 -0.21903947 0.846841083 -0.1934094065
## T_sanctus_B60184 0.165353303 -0.28421931 0.320185940 -0.2418419519
## T_saurophagus_18929 -2.954752435 -1.03336483 -7.482485044 -3.9973953511
## T_saurophagus_27804 -3.429289348 -1.00428040 -6.415912920 -3.5290916896
## T_saurophagus_36179 -3.355925085 -1.13790366 -7.540127253 -3.9140481492
## T_saurophagus_36283 -2.362801891 -0.84872019 -5.540059078 -2.6751985654
## T_saurophagus_36284 -3.332368002 -1.12638149 -7.342750750 -3.9642260666
## T_saurophagus_69666 -1.834807231 -0.59304316 -4.163051588 -2.0857800849
## T_sordidus_B33717 0.308450293 0.90065654 -0.467984537 0.0437621241
## T_sordidus_B33718 0.081083467 1.00244511 -0.989100600 0.1593810135
## T_sordidus_B33719 0.235714149 0.71952140 -0.866781567 -0.0333681844
## T_sordidus_B33720 0.101320778 -0.04270858 -0.835610426 -0.0940463399
## T_sordidus_B44198 0.007538713 1.17926063 0.197368280 0.2364324374
## T_sordidus_B44295 0.321157083 0.87501393 0.088792257 0.3402984846
## T_sordidus_B44296 -0.020835406 1.17018778 -0.106203915 0.3222657509
## T_sordidus_B51462 -0.171040247 0.27776856 -0.448898214 0.2738691827
## T_tristrami_18953 8.354048085 -1.08669113 -0.350613223 3.2701609773
## T_tristrami_27723 6.192153869 -1.06603337 -0.073821133 2.5628683585
## T_tristrami_27752 4.817998136 -1.04677148 -0.130292010 1.3850350699
## T_tristrami_27792 5.633309713 -0.33031051 0.817809323 1.6711763103
## T_tristrami_27793 7.199773895 -1.37875999 0.207708852 3.0424744034
## T_tristrami_32049 8.409930972 -0.67057013 -0.573285812 3.3109044403
## T_tristrami_33253 9.136560018 -1.15187021 -0.552318447 3.3272553021
## T_tristrami_33839 -0.420893960 0.09765055 -1.048826045 0.6470038549
## T_tristrami_33858 -0.317156551 0.28541825 -0.069643615 0.1839284256
## T_tristrami_33864 -0.270017088 -0.63525205 0.133391690 0.5797574521
## T_tristrami_33867 -0.025638437 0.45603646 -0.310440815 -0.6545402410
## T_tristrami_33895 0.351581509 0.71497501 0.233066440 -0.4798081973
## T_tristrami_36188 7.555056623 -1.04837374 -0.180029405 3.0483033291
## T_tristrami_6704 8.036260078 -0.55726935 -0.228551752 3.3689367841
## PC9 PC10 pop missing
## T_albicilla_22581 -0.052900091 0.322741756 albicilla 0.039455096
## T_albicilla_22591 -0.084307455 0.366213644 albicilla 0.014631685
## T_albicilla_22592 -0.015858408 0.304133631 albicilla 0.026841574
## T_albicilla_22611 -0.394697282 0.240497899 albicilla 0.284157417
## T_albicilla_85104 0.001673160 0.251239927 albicilla 0.048234107
## T_albicilla_85105 -0.106227942 0.330398468 albicilla 0.047830474
## T_chloris_12584 -0.223552668 0.269403805 chloris 0.009788093
## T_chloris_12606 0.111351513 0.210269782 chloris 0.037336024
## T_chloris_13960 0.354942817 -0.565684390 chloris 0.029061554
## T_chloris_14446 0.377229416 -0.041821008 chloris 0.015842583
## T_chloris_20983 0.352591311 -0.339831921 chloris 0.018567104
## T_chloris_22075 0.139492276 0.513491279 chloris 0.015035318
## T_chloris_23253 0.106396714 0.475215290 chloris 0.076387487
## T_chloris_23630 0.037286129 0.001475619 chloris 0.118668012
## T_chloris_23632 -0.131027033 0.104445175 chloris 0.118970737
## T_chloris_24382 0.017087988 0.360150382 chloris 0.089404642
## T_chloris_24727 -0.091584083 0.211530394 chloris 0.134207871
## T_colonus_2003089 -0.466510729 0.422280140 colonus 0.122603431
## T_colonus_2003097 -0.637862462 0.371211622 colonus 0.105449041
## T_colonus_2004070 -0.565934853 0.322423118 colonus 0.124924319
## T_leucopygius_32019 -0.173963753 0.081663736 leucopygius 0.117356206
## T_leucopygius_32037 0.334326700 -0.471519637 leucopygius 0.369323915
## T_leucopygius_34505 -0.003790306 0.318310947 leucopygius 0.101715439
## T_leucopygius_34508 0.577603668 -0.648716308 leucopygius 0.306659939
## T_leucopygius_DOT6654 -0.688769854 0.183155475 leucopygius 0.157013118
## T_sanctus_14877 4.017362746 -5.461522584 sanctus 0.043995964
## T_sanctus_14879 1.204709714 -1.284191667 sanctus 0.339051463
## T_sanctus_24565 -1.024012997 1.094588148 sanctus 0.015136226
## T_sanctus_25117 -1.076606255 0.510553040 sanctus 0.082038345
## T_sanctus_33267 -0.476017154 1.650413223 sanctus 0.026135217
## T_sanctus_34636 -12.589934563 -5.274328850 sanctus 0.025428860
## T_sanctus_34659 1.154880365 3.794758780 sanctus 0.248839556
## T_sanctus_35549 -1.025439805 1.216998130 sanctus 0.087991927
## T_sanctus_72545 0.441631446 0.970165121 sanctus 0.045408678
## T_sanctus_7567 0.271301414 2.579273716 sanctus 0.028456105
## T_sanctus_B29435 0.021439598 0.433001189 sanctus 0.097578204
## T_sanctus_B32637 0.662512715 1.723735002 sanctus 0.281130172
## T_sanctus_B33280 0.134988621 3.618571520 sanctus 0.153077699
## T_sanctus_B34636 -12.482978590 -5.147555782 sanctus 0.033905146
## T_sanctus_B34659 1.480150901 5.577428634 sanctus 0.042381433
## T_sanctus_B34946 -1.039375900 0.618823166 sanctus 0.047023209
## T_sanctus_B43266 0.455076212 0.799674015 sanctus 0.097578204
## T_sanctus_B50292 1.175622795 3.951464961 sanctus 0.083854692
## T_sanctus_B50543 0.086830128 1.958278059 sanctus 0.017860747
## T_sanctus_B51072 0.580018587 1.286692316 sanctus 0.014328961
## T_sanctus_B53055 -0.957151286 0.633320743 sanctus 0.254187689
## T_sanctus_B53068 -0.570247254 1.427888709 sanctus 0.059334006
## T_sanctus_B54673 0.231623813 1.794731702 sanctus 0.042482341
## T_sanctus_B57402 0.640068170 1.448941103 sanctus 0.190413724
## T_sanctus_B59372 -0.373745803 2.623081494 sanctus 0.008476287
## T_sanctus_B60180 3.215068103 -3.989047376 sanctus 0.255297679
## T_sanctus_B60181 4.269993134 -5.747485791 sanctus 0.085973764
## T_sanctus_B60182 3.501039271 -6.634343165 sanctus 0.010797175
## T_sanctus_B60183 4.603419044 -7.329570051 sanctus 0.019172553
## T_sanctus_B60184 4.420949020 -5.946555363 sanctus 0.011503532
## T_saurophagus_18929 0.134946906 -0.488372022 saurophagus 0.024520686
## T_saurophagus_27804 0.094509531 -0.510629865 saurophagus 0.015237134
## T_saurophagus_36179 0.092665120 -0.528368321 saurophagus 0.015539859
## T_saurophagus_36283 0.217080279 -0.389168951 saurophagus 0.251463169
## T_saurophagus_36284 0.137792886 -0.565139745 saurophagus 0.007870838
## T_saurophagus_69666 0.093721876 -0.180880885 saurophagus 0.381432896
## T_sordidus_B33717 -0.004682335 -0.331531463 sordidus 0.017860747
## T_sordidus_B33718 -0.215913545 0.065241856 sordidus 0.016548940
## T_sordidus_B33719 -0.730550289 -0.365917932 sordidus 0.135216953
## T_sordidus_B33720 -0.562784815 -0.555068407 sordidus 0.146922301
## T_sordidus_B44198 0.038921420 0.177124027 sordidus 0.131886983
## T_sordidus_B44295 0.742813349 -0.027004728 sordidus 0.069929364
## T_sordidus_B44296 0.315676735 -0.075786509 sordidus 0.161755802
## T_sordidus_B51462 0.143493047 -0.045086290 sordidus 0.076892028
## T_tristrami_18953 -0.003983793 -0.054350021 tristrami 0.030272452
## T_tristrami_27723 0.095332438 -0.270971110 tristrami 0.135721493
## T_tristrami_27752 -0.346754072 -0.119697034 tristrami 0.388092836
## T_tristrami_27792 0.428510103 -0.586606602 tristrami 0.256710394
## T_tristrami_27793 0.361864847 -0.340767726 tristrami 0.061150353
## T_tristrami_32049 -0.442321360 0.227506853 tristrami 0.030070636
## T_tristrami_33253 0.013433850 0.006098795 tristrami 0.009081736
## T_tristrami_33839 -0.813052247 1.707067864 tristrami 0.022300706
## T_tristrami_33858 0.727865546 0.713864412 tristrami 0.285771948
## T_tristrami_33864 0.301343335 2.279301422 tristrami 0.015237134
## T_tristrami_33867 -0.043567689 3.015457477 tristrami 0.017860747
## T_tristrami_33895 -0.160271635 1.211543462 tristrami 0.178607467
## T_tristrami_36188 -0.441053456 -0.197016113 tristrami 0.127951564
## T_tristrami_6704 0.098793004 -0.261303412 tristrami 0.041775984
##
## [[3]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 5.6452390 -8.41239840 -5.26281901 2.035329274
## T_albicilla_22591 5.6832063 -8.33728683 -5.24203958 1.964060555
## T_albicilla_22592 5.6831131 -8.26086973 -5.08093255 1.834000232
## T_albicilla_22611 4.0539320 -5.46903998 -3.46666627 1.380183607
## T_albicilla_85104 5.6950096 -8.38543637 -5.22059915 1.841820295
## T_albicilla_85105 5.6514486 -8.13088805 -5.07694529 1.731437790
## T_chloris_12584 2.6846536 -2.43618609 7.15034669 -5.056849236
## T_chloris_12606 2.7878221 -2.42676963 6.62837541 -5.554308113
## T_chloris_13960 2.5905652 -2.78419132 6.87121164 -8.078667197
## T_chloris_14446 2.5362635 -2.44885951 6.66128381 -7.180251996
## T_chloris_20983 2.5663595 -2.48004348 7.02702548 -7.488778660
## T_chloris_22075 2.7413150 -2.41049636 7.67349655 -5.387969736
## T_chloris_23253 2.6999684 -2.61643005 6.81559769 -4.756401022
## T_chloris_23630 2.7380806 -3.10671890 5.66416156 -7.542775187
## T_chloris_23632 2.6605392 -2.83783507 5.20594517 -6.765861129
## T_chloris_24382 2.5032655 -2.11360717 6.70102646 -4.950189873
## T_chloris_24727 2.5081048 -2.09734408 6.97947307 -4.640618985
## T_colonus_2003089 3.1443937 -3.67345991 -0.17831535 -1.166091537
## T_colonus_2003097 3.0834069 -3.50141322 0.02831708 -1.443139403
## T_colonus_2004070 3.1339628 -3.78798452 -0.87987061 -1.616569058
## T_leucopygius_32019 -28.5543271 -8.19034114 -0.57740988 0.005705525
## T_leucopygius_32037 -20.2695617 -5.96639578 -0.13225300 -0.167211416
## T_leucopygius_34505 -29.5935790 -8.42680422 -0.78681096 0.074590332
## T_leucopygius_34508 -22.6930469 -6.91718582 -0.15226248 -0.124307186
## T_leucopygius_DOT6654 -27.7871292 -8.11335368 -0.59868985 0.072632644
## T_sanctus_14877 -0.5578654 6.23810445 -1.44576024 -0.604079601
## T_sanctus_14879 -0.2962484 4.35558041 -1.09121575 -0.474037780
## T_sanctus_24565 -0.3500885 6.74262764 -1.88967712 0.180470651
## T_sanctus_25117 -0.7149583 6.19497469 -2.12784709 -0.007793604
## T_sanctus_33267 -0.6522212 6.59063409 -1.50670937 -0.228983896
## T_sanctus_34636 -0.6336239 7.19028431 -1.72124869 -0.581490192
## T_sanctus_34659 -0.2843195 4.97957835 -1.29233089 0.155135766
## T_sanctus_35549 -0.4853389 6.05294816 -1.39148974 -0.244293553
## T_sanctus_72545 -0.5153050 6.45251560 -1.60174978 0.124121799
## T_sanctus_7567 -0.6667380 7.08406971 -1.32357662 0.066595532
## T_sanctus_B29435 -0.3964496 6.17258882 -2.51088713 -0.340629738
## T_sanctus_B32637 -0.6536034 5.60635033 -1.39293920 -0.311172006
## T_sanctus_B33280 -0.7486419 6.84296250 -2.40397402 -0.257011168
## T_sanctus_B34636 -0.6984801 7.33580858 -1.88758344 -0.343291544
## T_sanctus_B34659 -1.0137437 7.25110359 -2.33732993 0.112295065
## T_sanctus_B34946 -0.5974342 6.66159533 -1.86046646 -0.261562502
## T_sanctus_B43266 -0.7086985 6.48204652 -2.18159280 0.053863580
## T_sanctus_B50292 -0.9373012 7.13993890 -1.95658421 0.098770471
## T_sanctus_B50543 -0.9138289 6.56875252 -2.15878677 -0.196626903
## T_sanctus_B51072 -0.6883753 6.71811696 -2.45402180 0.213218337
## T_sanctus_B53055 -0.4120105 5.23177019 -1.47034402 0.169967841
## T_sanctus_B53068 -0.7475792 6.17845897 -1.54354742 -0.430702482
## T_sanctus_B54673 -0.5289031 6.73179896 -1.79177139 0.368406671
## T_sanctus_B57402 -0.5652764 6.32228754 -2.08732841 0.104600591
## T_sanctus_B59372 -0.5864496 6.59083791 -1.92560723 -0.110646991
## T_sanctus_B60180 -0.6196309 6.06787861 -1.78001059 -1.000836161
## T_sanctus_B60181 -0.8673624 7.17337090 -2.18235958 -0.347033485
## T_sanctus_B60182 -0.8048558 7.27912615 -1.88117555 0.133661905
## T_sanctus_B60183 -0.3994268 7.22178366 -2.32744705 -0.322094373
## T_sanctus_B60184 -0.7719923 7.54493985 -1.14582570 -0.066485887
## T_saurophagus_18929 5.5132942 -8.04261261 -5.63566251 1.492370799
## T_saurophagus_27804 5.5214192 -8.09568247 -5.26950425 1.539493225
## T_saurophagus_36179 5.6151762 -8.38941474 -5.96067220 1.688784914
## T_saurophagus_36283 4.6658259 -7.16752488 -4.64332181 1.223193116
## T_saurophagus_36284 5.4693665 -8.15390171 -5.77216977 1.661716649
## T_saurophagus_69666 3.3525662 -4.69335973 -2.77738586 0.852616743
## T_sordidus_B33717 1.5761060 -0.13870149 9.70225414 7.948231139
## T_sordidus_B33718 1.6850676 -0.14989923 9.51437039 7.488878763
## T_sordidus_B33719 1.4483052 -0.09149056 8.95774046 7.693513421
## T_sordidus_B33720 1.2605462 -0.07077542 8.89658074 7.621189804
## T_sordidus_B44198 1.5419871 -0.32152071 8.57288555 7.102565118
## T_sordidus_B44295 1.6163416 -0.64330257 8.05555711 6.960627102
## T_sordidus_B44296 1.4596427 -0.68341290 8.38375556 6.934516010
## T_sordidus_B51462 1.6637220 -0.41529467 9.16440935 7.640017509
## T_tristrami_18953 4.7172294 -6.91514875 -2.58663475 -0.326577371
## T_tristrami_27723 4.1717161 -6.45193956 -2.43340836 -0.128146007
## T_tristrami_27752 3.1451754 -4.78831908 -1.56984250 -0.353897001
## T_tristrami_27792 3.3021500 -4.83500889 -1.19515277 -0.546426632
## T_tristrami_27793 4.2613683 -6.08006682 -1.86041957 -0.025182308
## T_tristrami_32049 4.5929769 -6.60603734 -2.16839134 -0.429173135
## T_tristrami_33253 4.5779882 -6.54607787 -2.53277078 -0.073025990
## T_tristrami_33839 -0.9543847 6.85923067 -1.68578019 0.481560667
## T_tristrami_33858 -0.3119779 4.70850068 -0.95433080 0.121307620
## T_tristrami_33864 -0.6757799 6.70611009 -1.67828205 -0.860612589
## T_tristrami_33867 -0.8177934 6.82717865 -1.60988412 0.248672051
## T_tristrami_33895 -0.7243216 6.15084225 -1.63893544 -0.579365561
## T_tristrami_36188 4.3312600 -6.37494009 -2.54459633 -0.009552161
## T_tristrami_6704 4.9187719 -7.26892518 -2.80986655 -0.039402760
## PC5 PC6 PC7 PC8
## T_albicilla_22581 -5.187871133 -1.252012984 5.868196792 1.172802662
## T_albicilla_22591 -5.475395276 -1.128759865 5.793743674 1.154487096
## T_albicilla_22592 -5.410654039 -1.136945397 5.544712352 0.992730260
## T_albicilla_22611 -3.436596619 -1.076745470 4.247722523 0.816650132
## T_albicilla_85104 -5.225230015 -1.138642082 4.962736135 0.564182901
## T_albicilla_85105 -5.143589157 -0.988940167 4.814554622 0.420048209
## T_chloris_12584 -1.073910441 6.301226302 1.381556673 -1.918244501
## T_chloris_12606 -0.919165979 5.583663708 1.904823594 -1.890576504
## T_chloris_13960 -1.989115710 -5.698881885 -1.928914277 2.987328330
## T_chloris_14446 -2.056426791 -6.011526064 -1.913209523 2.960184204
## T_chloris_20983 -2.088036289 -5.478183926 -1.906589669 3.169079048
## T_chloris_22075 -1.050603902 6.088493935 1.513835445 -1.830661999
## T_chloris_23253 -1.071593976 5.112560223 1.286828795 -1.643986041
## T_chloris_23630 -2.550228654 -4.885167773 -2.094963128 3.041897216
## T_chloris_23632 -2.481480546 -4.401558908 -1.717070754 2.644626220
## T_chloris_24382 -1.194326060 6.325748589 1.621516468 -2.087241976
## T_chloris_24727 -0.911347086 6.158017666 1.733724004 -2.038927912
## T_colonus_2003089 4.059206243 -5.472603190 0.991323177 -9.605343901
## T_colonus_2003097 3.569836845 -5.361617031 0.830047833 -9.415367393
## T_colonus_2004070 4.303180097 -5.116517779 1.174000610 -9.503447539
## T_leucopygius_32019 -0.168434108 0.021870150 0.025207383 0.062678297
## T_leucopygius_32037 0.019221328 -0.179073287 0.431639493 0.169718473
## T_leucopygius_34505 -0.114865050 0.223827695 -0.230804917 -0.055377050
## T_leucopygius_34508 -0.160703665 0.204769986 0.162172164 -0.090001484
## T_leucopygius_DOT6654 -0.200379826 -0.010336040 -0.025040845 -0.049239561
## T_sanctus_14877 -0.217208700 0.431333149 0.608908303 -0.395260844
## T_sanctus_14879 -0.304523223 -0.115839209 -0.060370963 -0.495003236
## T_sanctus_24565 -0.040539343 0.247368204 -0.189068286 0.099526651
## T_sanctus_25117 -0.141171496 0.128955346 -0.178322930 -0.088329056
## T_sanctus_33267 -0.183485960 0.125512166 -0.014672092 -0.188564599
## T_sanctus_34636 -0.465430889 0.509877157 -0.004979664 -0.071574696
## T_sanctus_34659 0.067296968 -0.448216740 -0.288492516 0.169088295
## T_sanctus_35549 -0.030866471 -0.082306717 -0.306435535 0.279440505
## T_sanctus_72545 -0.048083257 -0.012863752 0.072042681 0.590280977
## T_sanctus_7567 0.119339420 0.125721170 0.039521461 0.074364431
## T_sanctus_B29435 0.052245331 -0.288802845 -0.204215998 -0.376239933
## T_sanctus_B32637 0.068175440 0.330860039 -0.151456828 -0.195507815
## T_sanctus_B33280 -0.015624120 0.284937345 -0.291046736 0.918589761
## T_sanctus_B34636 -0.420458237 0.352086525 -0.035991582 0.010892006
## T_sanctus_B34659 0.220552451 0.027063610 -0.280865914 0.361299954
## T_sanctus_B34946 -0.190988722 0.419687731 0.009618425 0.454898412
## T_sanctus_B43266 0.067673358 0.215517473 -0.012783980 -0.311374731
## T_sanctus_B50292 -0.162942498 -0.112553991 -0.256012697 0.785284399
## T_sanctus_B50543 -0.004352241 -0.031191841 -0.209473259 -0.208793775
## T_sanctus_B51072 0.065084705 -0.224718304 0.757967590 -0.006269405
## T_sanctus_B53055 -0.405967920 0.532034142 0.418081253 0.511449284
## T_sanctus_B53068 -0.648150939 0.057614147 -0.384774110 0.647672407
## T_sanctus_B54673 -0.683073699 -0.193372469 -0.100939843 0.164717773
## T_sanctus_B57402 -0.579434870 -0.181866570 -0.085951742 0.625164190
## T_sanctus_B59372 -0.011637982 0.419671285 -0.477883906 0.951599263
## T_sanctus_B60180 0.201644708 0.061470490 0.699596042 -0.489558384
## T_sanctus_B60181 0.192273163 0.059571296 1.098574967 0.020020999
## T_sanctus_B60182 0.547881247 -0.006171584 0.409798559 -0.219801797
## T_sanctus_B60183 -0.239054192 0.384633679 0.896758369 -0.368345945
## T_sanctus_B60184 0.330240813 0.187713705 0.161062861 -0.604896978
## T_saurophagus_18929 -3.218245686 1.829348602 -6.926869936 -1.443689591
## T_saurophagus_27804 -3.623475782 1.750601397 -5.868828012 -1.399275416
## T_saurophagus_36179 -3.634958370 1.954825669 -6.895045124 -1.422188412
## T_saurophagus_36283 -2.941394644 1.604669391 -5.193523780 -1.109702518
## T_saurophagus_36284 -3.471219475 1.903295845 -6.629480668 -1.395568772
## T_saurophagus_69666 -1.935039667 0.974300899 -3.638063546 -0.326245669
## T_sordidus_B33717 0.071063847 -0.642628401 -0.222962523 0.007924132
## T_sordidus_B33718 0.009184373 -1.004820706 -0.687835214 -0.054461622
## T_sordidus_B33719 -0.236151131 -0.598265195 -0.605673098 0.228194378
## T_sordidus_B33720 -0.051496197 -0.201960926 -0.374413866 -0.149156690
## T_sordidus_B44198 -0.061776521 -0.947790668 -0.065449430 0.492931368
## T_sordidus_B44295 0.030219066 -0.673838885 -0.135114024 0.935811455
## T_sordidus_B44296 0.088415012 -0.959526166 -0.336104241 0.687395274
## T_sordidus_B51462 -0.276133384 -0.339301440 -0.441548472 0.113108000
## T_tristrami_18953 7.314117052 0.718071212 0.269303675 2.628917902
## T_tristrami_27723 5.948277198 0.981196086 0.477412506 2.241717401
## T_tristrami_27752 4.683542112 0.859718835 0.159292595 1.165263271
## T_tristrami_27792 5.317267532 0.121372233 1.017669241 1.311897481
## T_tristrami_27793 6.456514484 1.125004108 0.870682594 2.472781154
## T_tristrami_32049 7.392861892 0.503135391 -0.200569713 2.684833086
## T_tristrami_33253 7.588030614 0.835141394 -0.050682755 2.515580934
## T_tristrami_33839 -0.425729809 -0.091653563 -0.766941631 0.911439538
## T_tristrami_33858 -0.186798363 -0.595010735 -0.179071928 0.373018709
## T_tristrami_33864 -0.144920396 0.537777206 0.416176238 0.373965453
## T_tristrami_33867 -0.047364089 -0.117391202 -0.520720508 0.086795773
## T_tristrami_33895 0.380216834 -0.634635783 -0.183166104 -0.224881707
## T_tristrami_36188 6.602850878 0.704474069 0.455542287 2.846157914
## T_tristrami_6704 7.191239585 0.517500291 0.146044883 2.774671876
## PC9 PC10 pop missing
## T_albicilla_22581 0.218280865 -0.06200242 albicilla 0.019246299
## T_albicilla_22591 0.206500293 0.05967875 albicilla 0.007537012
## T_albicilla_22592 0.227380433 0.05729810 albicilla 0.016016151
## T_albicilla_22611 0.270618918 -0.02441943 albicilla 0.265545087
## T_albicilla_85104 0.157866365 0.04104670 albicilla 0.031493943
## T_albicilla_85105 0.265754851 0.05674464 albicilla 0.030955585
## T_chloris_12584 0.164203769 0.08123257 chloris 0.006729475
## T_chloris_12606 -0.063731663 0.29209332 chloris 0.022745626
## T_chloris_13960 -0.714491994 -0.32828869 chloris 0.019919246
## T_chloris_14446 -0.432151826 0.04357376 chloris 0.011574697
## T_chloris_20983 -0.646826205 -0.21226387 chloris 0.012382234
## T_chloris_22075 0.384291356 0.61233231 chloris 0.011440108
## T_chloris_23253 0.267422646 0.56224343 chloris 0.047240915
## T_chloris_23630 0.067148309 -0.12363291 chloris 0.060430686
## T_chloris_23632 0.237977087 -0.22243591 chloris 0.094481830
## T_chloris_24382 0.538039905 0.36839134 chloris 0.062718708
## T_chloris_24727 0.464376727 -0.02477160 chloris 0.110228802
## T_colonus_2003089 0.708257619 0.32452160 colonus 0.100269179
## T_colonus_2003097 0.701004867 -0.09941303 colonus 0.076312248
## T_colonus_2004070 0.814499693 0.13486173 colonus 0.107133244
## T_leucopygius_32019 0.057600545 -0.07115051 leucopygius 0.106594886
## T_leucopygius_32037 -0.253111050 0.37284323 leucopygius 0.371601615
## T_leucopygius_34505 0.022199862 -0.18129032 leucopygius 0.092328398
## T_leucopygius_34508 -0.659220776 0.04132618 leucopygius 0.300538358
## T_leucopygius_DOT6654 0.533886070 -0.28838475 leucopygius 0.140376851
## T_sanctus_14877 -6.148414644 -1.21455015 sanctus 0.030013459
## T_sanctus_14879 -1.708850136 -0.02916317 sanctus 0.330148048
## T_sanctus_24565 0.922055377 0.48996849 sanctus 0.010497981
## T_sanctus_25117 1.038178741 -0.32254842 sanctus 0.066083445
## T_sanctus_33267 2.009101313 0.29878256 sanctus 0.020053836
## T_sanctus_34636 3.888586601 -10.85882464 sanctus 0.017227456
## T_sanctus_34659 1.535323963 2.25764396 sanctus 0.229609690
## T_sanctus_35549 1.425720384 0.44593167 sanctus 0.066352624
## T_sanctus_72545 0.708625854 0.57667174 sanctus 0.032839838
## T_sanctus_7567 1.129673040 1.61702003 sanctus 0.018438762
## T_sanctus_B29435 0.153078770 0.71669814 sanctus 0.053566622
## T_sanctus_B32637 0.974244529 1.62145839 sanctus 0.200942127
## T_sanctus_B33280 2.404304370 2.34731277 sanctus 0.092193809
## T_sanctus_B34636 3.841384171 -10.81045654 sanctus 0.018169583
## T_sanctus_B34659 2.328706498 3.29425115 sanctus 0.023553163
## T_sanctus_B34946 1.331850785 -0.47942460 sanctus 0.025841184
## T_sanctus_B43266 -0.416035955 1.32928141 sanctus 0.046837147
## T_sanctus_B50292 2.428835014 3.15413651 sanctus 0.049932705
## T_sanctus_B50543 1.301963257 1.17457457 sanctus 0.017092867
## T_sanctus_B51072 0.169705831 1.70365551 sanctus 0.011305518
## T_sanctus_B53055 1.279758235 -0.57994924 sanctus 0.185464334
## T_sanctus_B53068 0.804539212 0.23140818 sanctus 0.037146703
## T_sanctus_B54673 0.392227872 1.13691549 sanctus 0.026110363
## T_sanctus_B57402 0.784842325 1.49756464 sanctus 0.115343203
## T_sanctus_B59372 2.300602522 1.56737742 sanctus 0.006325707
## T_sanctus_B60180 -4.776190890 -0.49712510 sanctus 0.169582773
## T_sanctus_B60181 -6.428820889 -1.14000183 sanctus 0.041857335
## T_sanctus_B60182 -6.472170959 -1.49111266 sanctus 0.008613728
## T_sanctus_B60183 -7.029579520 -1.19923968 sanctus 0.011440108
## T_sanctus_B60184 -5.996487561 -0.85358896 sanctus 0.009017497
## T_saurophagus_18929 -0.474336155 -0.03473073 saurophagus 0.013458950
## T_saurophagus_27804 -0.509792245 -0.11609298 saurophagus 0.007133244
## T_saurophagus_36179 -0.537234555 -0.10821649 saurophagus 0.005921938
## T_saurophagus_36283 -0.542517962 -0.13684638 saurophagus 0.174158816
## T_saurophagus_36284 -0.556998592 -0.06730314 saurophagus 0.002153432
## T_saurophagus_69666 -0.003215092 0.10187968 saurophagus 0.386944818
## T_sordidus_B33717 -0.361236315 -0.29142262 sordidus 0.012920592
## T_sordidus_B33718 -0.153431878 -0.05647432 sordidus 0.014939435
## T_sordidus_B33719 -0.237039393 -0.66568513 sordidus 0.081426649
## T_sordidus_B33720 -0.200962613 -0.64280175 sordidus 0.088425303
## T_sordidus_B44198 0.260746420 0.09649012 sordidus 0.074562584
## T_sordidus_B44295 -0.190650914 0.38323511 sordidus 0.051951548
## T_sordidus_B44296 0.045680569 0.39539206 sordidus 0.096096904
## T_sordidus_B51462 0.047079200 -0.07830341 sordidus 0.036473755
## T_tristrami_18953 0.240052074 -0.17553615 tristrami 0.017631225
## T_tristrami_27723 -0.267470617 0.01763533 tristrami 0.080619112
## T_tristrami_27752 -0.015940875 -0.16979356 tristrami 0.303499327
## T_tristrami_27792 -0.574525468 -0.12805275 tristrami 0.216419919
## T_tristrami_27793 -0.499361958 0.11628532 tristrami 0.041588156
## T_tristrami_32049 0.415561436 -0.33476624 tristrami 0.021130552
## T_tristrami_33253 0.032609399 -0.05234804 tristrami 0.006056528
## T_tristrami_33839 1.514005547 0.61558295 tristrami 0.011574697
## T_tristrami_33858 0.329704623 0.83523258 tristrami 0.204845222
## T_tristrami_33864 1.513544509 1.42010639 tristrami 0.015074024
## T_tristrami_33867 1.910056047 1.47392616 tristrami 0.008882907
## T_tristrami_33895 0.914015181 0.98036321 tristrami 0.114939435
## T_tristrami_36188 0.055514246 -0.43655638 tristrami 0.074831763
## T_tristrami_6704 0.131610608 -0.33600069 tristrami 0.023283984evaluate the effect of missing data using splitstree
#set two potential cutoffs
vcfRa<-missing_by_snp(vcfR, cutoff = .8)## cutoff is specified, filtered vcfR object will be returned## 87.73% of SNPs fell below a completeness cutoff of 0.8 and were removed from the VCF
vcfRb<-missing_by_snp(vcfR, cutoff = .85)## cutoff is specified, filtered vcfR object will be returned## 90.8% of SNPs fell below a completeness cutoff of 0.85 and were removed from the VCF
#convert each to genlight
gena<-vcfR2genlight(vcfRa)
genb<-vcfR2genlight(vcfRb)
#output pairwise difference matrix for each to run splitstree
gena@ind.names<-gsub(gena@ind.names, pattern = "T_", replacement = "")
gena@ind.names<-gsub(gena@ind.names, pattern = "_", replacement = "")
gena@ind.names<-gsub(gena@ind.names, pattern = "albicilla", replacement = "alb")
gena@ind.names<-gsub(gena@ind.names, pattern = "chloris", replacement = "chlor")
gena@ind.names<-gsub(gena@ind.names, pattern = "colonus", replacement = "col")
gena@ind.names<-gsub(gena@ind.names, pattern = "sanctus", replacement = "san")
gena@ind.names<-gsub(gena@ind.names, pattern = "saurophagus", replacement = "saur")
gena@ind.names<-gsub(gena@ind.names, pattern = "sordidus", replacement = "sord")
gena@ind.names<-gsub(gena@ind.names, pattern = "tristrami", replacement = "tris")
gena@ind.names<-gsub(gena@ind.names, pattern = "leucopygius", replacement = "leu")
gena@ind.names<-gsub(gena@ind.names, pattern = "DOT", replacement = "D")
gena@ind.names## [1] "alb22581" "alb22591" "alb22592" "alb22611" "alb85104"
## [6] "alb85105" "chlor12584" "chlor12606" "chlor13960" "chlor14446"
## [11] "chlor20983" "chlor22075" "chlor23253" "chlor23630" "chlor23632"
## [16] "chlor24382" "chlor24727" "col2003089" "col2003097" "col2004070"
## [21] "leu32019" "leu32037" "leu34505" "leu34508" "leuD6654"
## [26] "san14877" "san14879" "san24565" "san25117" "san33267"
## [31] "san34636" "san34659" "san35549" "san72545" "san7567"
## [36] "sanB29435" "sanB32637" "sanB33280" "sanB34636" "sanB34659"
## [41] "sanB34946" "sanB43266" "sanB50292" "sanB50543" "sanB51072"
## [46] "sanB53055" "sanB53068" "sanB54673" "sanB57402" "sanB59372"
## [51] "sanB60180" "sanB60181" "sanB60182" "sanB60183" "sanB60184"
## [56] "saur18929" "saur27804" "saur36179" "saur36283" "saur36284"
## [61] "saur69666" "sordB33717" "sordB33718" "sordB33719" "sordB33720"
## [66] "sordB44198" "sordB44295" "sordB44296" "sordB51462" "tris18953"
## [71] "tris27723" "tris27752" "tris27792" "tris27793" "tris32049"
## [76] "tris33253" "tris33839" "tris33858" "tris33864" "tris33867"
## [81] "tris33895" "tris36188" "tris6704"pop(gena)<-popmap$pop
sample.div.80 <- stamppNeisD(gena, pop = FALSE)
#export for splitstree
#stamppPhylip(distance.mat=sample.div.80, file="~/Desktop/todi.2022/todi.80.splits.txt")
#80% completeness cutoff splitstree
knitr::include_graphics(c("/Users/devder/Desktop/todi.2022/todi.80.splitstree.png"))
#repeat for 85% cutoff
#output pairwise difference matrix for each to run splitstree
genb@ind.names<-gena@ind.names
pop(genb)<-popmap$pop
sample.div.85 <- stamppNeisD(genb, pop = FALSE)
#export for splitstree
#stamppPhylip(distance.mat=sample.div.85, file="~/Desktop/todi.2022/todi.85.splits.txt")
#85% completeness cutoff splitstree
knitr::include_graphics(c("/Users/devder/Desktop/todi.2022/todi.85.splitstree.png"))
#repeat with removing singletons
vcfR.mac<-min_mac(vcfRa, min.mac = 2)## 28.31% of SNPs fell below a minor allele count of 2 and were removed from the VCF
genc<-vcfR2genlight(vcfR.mac)
genc@ind.names<-gena@ind.names
pop(genc)<-popmap$pop
sample.div <- stamppNeisD(genc, pop = FALSE)
#export for splitstree
#stamppPhylip(distance.mat=sample.div, file="~/Desktop/todi.2022/todi.80.min.mac.splits.txt")
#80% completeness cutoff with min.mac splitstree
knitr::include_graphics(c("/Users/devder/Desktop/todi.2022/todi.80.mac.splitstree.png"))
#the three splitstrees are nearly identical. I am satisfied that neither missing data nor singletons are driving patterns of sample relatedness/assignment. We will keep the 85% complete dataset without a minor allele filter for downstream analyses because it looks the cleanest.#plot depth per snp and per sample
dp <- extract.gt(vcfRa, element = "DP", as.numeric=TRUE)
heatmap.bp(dp, rlabels = FALSE)
#plot genotype quality per snp and per sample
gq <- extract.gt(vcfRa, element = "GQ", as.numeric=TRUE)
heatmap.bp(gq, rlabels = FALSE)
###We can use the convenient function ‘write.vcf’ from vcfR to export our filtered vcf file for downstream analyses
#write out vcf
vcfR::write.vcf(vcfRb, file = "~/Desktop/todi.2022/todi.85.vcf.gz")
#perform linkage filtering to get a reduced vcf with only unlinked SNPs
vcfR.thin<-distance_thin(vcfRb, min.distance = 100)##
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|======================================================================| 100%## 1892 out of 7430 input SNPs were not located within 100 base-pairs of another SNP and were retained despite filteringvcfR.thin## ***** Object of Class vcfR *****
## 83 samples
## 32 CHROMs
## 1,892 variants
## Object size: 12.1 Mb
## 8.083 percent missing data
## ***** ***** *****vcfR::write.vcf(vcfR.thin, file = "~/Desktop/todi.2022/todi.unlinked.85.vcf.gz")